def layer_op(self, input_tensor, is_training=True):
"""
output is an elementwise sum of deconvolution and additive upsampling::
--(inputs)--o--deconvolution-------+--(outputs)--
| |
o--additive upsampling-o
:param input_tensor:
:param is_training:
:return: an upsampled tensor with ``n_input_channels/n_splits``
feature channels.
"""
n_output_chns = check_divisible_channels(input_tensor, self.n_splits)
# deconvolution path
deconv_output = Deconv(n_output_chns=n_output_chns,
with_bias=False, with_bn=True,
**self.deconv_param)(input_tensor, is_training)
# additive upsampling path
additive_output = AdditiveUpsampleLayer(
new_size=deconv_output.get_shape().as_list()[1:-1],
n_splits=self.n_splits)(input_tensor)
output_tensor = ElementwiseLayer('SUM')(deconv_output, additive_output)
return output_tensor
def layer_op(self, input_tensor, is_training=True):
"""
output is an elementwise sum of deconvolution and additive upsampling::
--(inputs)--o--deconvolution-------+--(outputs)--
| |
o--additive upsampling-o
:param input_tensor:
:param is_training:
:return: an upsampled tensor with ``n_input_channels/n_splits``
feature channels.
"""
n_output_chns = check_divisible_channels(input_tensor, self.n_splits)
# deconvolution path
deconv_output = Deconv(n_output_chns=n_output_chns,
with_bias=False, feature_normalization='batch',
**self.deconv_param)(input_tensor, is_training)
# additive upsampling path
additive_output = AdditiveUpsampleLayer(
new_size=deconv_output.get_shape().as_list()[1:-1],
n_splits=self.n_splits)(input_tensor)
output_tensor = ElementwiseLayer('SUM')(deconv_output, additive_output)
return output_tensor
def layer_op(self, input_tensor, is_training):
output_tensor = input_tensor
for (kernel_size, n_features) in zip(self.kernels, self.n_chns):
conv_op = ConvolutionalLayer(n_output_chns=n_features,
kernel_size=kernel_size,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='{}'.format(n_features),
padding='VALID',
with_bn=False,
with_bias=True)
output_tensor = conv_op(output_tensor, is_training)
if self.with_downsample_branch:
branch_output = output_tensor
else:
branch_output = None
if self.func == 'DOWNSAMPLE':
downsample_op = DownSampleLayer('MAX',
kernel_size=2,
stride=2,
name='down_2x_isotropic')
output_tensor = downsample_op(output_tensor)
if self.func == 'DOWNSAMPLE_ANISOTROPIC':
downsample_op = DownSampleLayer('MAX',
kernel_size=[2, 2, 1],
stride=[2, 2, 1],
name='down_2x2x1')
output_tensor = downsample_op(output_tensor)
elif self.func == 'UPSAMPLE':
upsample_op = DeconvolutionalLayer(n_output_chns=self.n_chns[-1],
kernel_size=2,
stride=2,
name='up_2x_isotropic',
with_bn=False,
with_bias=True)
output_tensor = upsample_op(output_tensor, is_training)
elif self.func == 'UPSAMPLE_ANISOTROPIC':
upsample_op = DeconvolutionalLayer(n_output_chns=self.n_chns[-1],
kernel_size=[2, 2, 1],
stride=[2, 2, 1],
name='up_2x2x1',
with_bn=False,
with_bias=True)
output_tensor = upsample_op(output_tensor, is_training)
elif self.func == 'NONE':
pass # do nothing
return output_tensor, branch_output
def up(ch, x):
with tf.name_scope('up'):
deconv_layer = DeconvolutionalLayer(ch,
3,
stride=2,
w_initializer=w_init)
return tf.nn.relu(deconv_layer(x, is_training=is_training))
def up(ch, x):
with tf.name_scope('up'):
deconv_layer = DeconvolutionalLayer(
n_output_chns=ch,
kernel_size=3,
stride=2,
with_bn=True,
with_bias=False,
acti_func='relu',
w_initializer=self.initializers['w'])
return deconv_layer(x, is_training=is_training)
def up(ch, x, hack=False):
with tf.name_scope('up'):
deconv = DeconvolutionalLayer(ch,
3,
with_bn=False,
stride=2,
w_initializer=w_init)(
x, is_training=is_training)
if hack:
deconv = deconv[:, :,
1:, :] # hack to match Yipeng's image size
return tf.nn.relu(tf.contrib.layers.batch_norm(deconv))
def up(ch, x):
"""
Performs deconvolution operation with kernel size 3, stride 2, batch norm, and relu
:param ch: int, number of output channels for deconvolutional layer
:param x: tensor, input to deconvolutional layer
:return: tensor, output of deconvolutiona layer
"""
with tf.name_scope('up'):
deconv_layer = DeconvolutionalLayer(
n_output_chns=ch,
kernel_size=3,
stride=2,
feature_normalization='batch',
with_bias=False,
acti_func='relu',
w_initializer=self.initializers['w'])
return deconv_layer(x, is_training=is_training)
def _test_deconv_layer_output_shape(self,
rank,
param_dict,
output_shape,
is_training=None,
dropout_prob=None):
if rank == 2:
input_data = self.get_2d_input()
elif rank == 3:
input_data = self.get_3d_input()
deconv_layer = DeconvolutionalLayer(**param_dict)
output_data = deconv_layer(input_data,
is_training=is_training,
keep_prob=dropout_prob)
print(deconv_layer)
with self.cached_session() as sess:
sess.run(tf.global_variables_initializer())
output_value = sess.run(output_data)
self.assertAllClose(output_shape, output_value.shape)
def layer_op(self, input_tensor, is_training):
"""
:param input_tensor: tensor, input to the UNet block
:param is_training: boolean, True if network is in training mode
:return: output tensor of the UNet block and branch before downsampling (if required)
"""
output_tensor = input_tensor
for (kernel_size, n_features) in zip(self.kernels, self.n_chns):
conv_op = ConvolutionalLayer(n_output_chns=n_features,
kernel_size=kernel_size,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='{}'.format(n_features))
output_tensor = conv_op(output_tensor, is_training)
if self.with_downsample_branch:
branch_output = output_tensor
else:
branch_output = None
if self.func == 'DOWNSAMPLE':
downsample_op = DownSampleLayer('MAX',
kernel_size=2,
stride=2,
name='down_2x2')
output_tensor = downsample_op(output_tensor)
elif self.func == 'UPSAMPLE':
upsample_op = DeconvolutionalLayer(n_output_chns=self.n_chns[-1],
kernel_size=2,
stride=2,
name='up_2x2')
output_tensor = upsample_op(output_tensor, is_training)
elif self.func == 'NONE':
pass # do nothing
return output_tensor, branch_output
def layer_op(self, images, is_training=True, layer_id=-1, **unused_kwargs):
"""
:param images: tensor to input to the network. Size has to be divisible by 8
:param is_training: boolean, True if network is in training mode
:param layer_id: int, index of the layer to return as output
:param unused_kwargs:
:return: output of layer indicated by layer_id
"""
assert (layer_util.check_spatial_dims(images, lambda x: x % 8 == 0))
# go through self.layers, create an instance of each layer
# and plugin data
layer_instances = []
### first convolution layer
params = self.layers[0]
first_conv_layer = ConvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
stride=2,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = first_conv_layer(images, is_training)
layer_instances.append((first_conv_layer, flow))
### resblocks, all kernels dilated by 1 (normal convolution)
params = self.layers[1]
with DilatedTensor(flow, dilation_factor=1) as dilated:
for j in range(params['repeat']):
res_block = HighResBlock(params['n_features'],
params['kernels'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='%s_%d' % (params['name'], j))
dilated.tensor = res_block(dilated.tensor, is_training)
layer_instances.append((res_block, dilated.tensor))
flow = dilated.tensor
### resblocks, all kernels dilated by 2
params = self.layers[2]
with DilatedTensor(flow, dilation_factor=2) as dilated:
for j in range(params['repeat']):
res_block = HighResBlock(params['n_features'],
params['kernels'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='%s_%d' % (params['name'], j))
dilated.tensor = res_block(dilated.tensor, is_training)
layer_instances.append((res_block, dilated.tensor))
flow = dilated.tensor
### resblocks, all kernels dilated by 4
params = self.layers[3]
with DilatedTensor(flow, dilation_factor=4) as dilated:
for j in range(params['repeat']):
res_block = HighResBlock(params['n_features'],
params['kernels'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='%s_%d' % (params['name'], j))
dilated.tensor = res_block(dilated.tensor, is_training)
layer_instances.append((res_block, dilated.tensor))
flow = dilated.tensor
### 1x1x1 convolution layer
params = self.layers[4]
fc_layer = ConvolutionalLayer(n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = fc_layer(flow, is_training)
layer_instances.append((fc_layer, flow))
### 3x3x3 deconvolution layer
params = self.layers[4]
fc_layer = DeconvolutionalLayer(n_output_chns=params['n_features'],
kernel_size=3,
stride=2,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='deconv')
flow = fc_layer(flow, is_training)
layer_instances.append((fc_layer, flow))
### 1x1x1 convolution layer
params = self.layers[5]
fc_layer = ConvolutionalLayer(n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
acti_func=None,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = fc_layer(flow, is_training)
layer_instances.append((fc_layer, flow))
# set training properties
if is_training:
self._print(layer_instances)
return layer_instances[-1][1]
return layer_instances[layer_id][1]
def layer_op(self, images, is_training):
block1_1 = ResBlock(self.base_chns[0],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block1_1')
block1_2 = ResBlock(self.base_chns[0],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block1_2')
block2_1 = ResBlock(self.base_chns[1],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block2_1')
block2_2 = ResBlock(self.base_chns[1],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block2_2')
block3_1 = ResBlock(self.base_chns[2],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 1, 1], [1, 1, 1]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block3_1')
block3_2 = ResBlock(self.base_chns[2],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 2, 2], [1, 2, 2]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block3_2')
block3_3 = ResBlock(self.base_chns[2],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block3_3')
block4_1 = ResBlock(self.base_chns[3],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block4_1')
block4_2 = ResBlock(self.base_chns[3],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 2, 2], [1, 2, 2]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block4_2')
block4_3 = ResBlock(self.base_chns[3],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 1, 1], [1, 1, 1]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block4_3')
fuse1 = ConvolutionalLayer(self.base_chns[0],
kernel_size=[3, 1, 1],
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='fuse1')
downsample1 = ConvolutionalLayer(self.base_chns[0],
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='downsample1')
fuse2 = ConvolutionalLayer(self.base_chns[1],
kernel_size=[3, 1, 1],
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='fuse2')
downsample2 = ConvolutionalLayer(self.base_chns[1],
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='downsample2')
fuse3 = ConvolutionalLayer(self.base_chns[2],
kernel_size=[3, 1, 1],
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='fuse3')
fuse4 = ConvolutionalLayer(self.base_chns[3],
kernel_size=[3, 1, 1],
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='fuse4')
feature_expand1 = ConvolutionalLayer(
self.base_chns[1],
kernel_size=[1, 1, 1],
stride=[1, 1, 1],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='feature_expand1')
feature_expand2 = ConvolutionalLayer(
self.base_chns[2],
kernel_size=[1, 1, 1],
stride=[1, 1, 1],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='feature_expand2')
feature_expand3 = ConvolutionalLayer(
self.base_chns[3],
kernel_size=[1, 1, 1],
stride=[1, 1, 1],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='feature_expand3')
centra_slice1 = TensorSliceLayer(margin=2)
centra_slice2 = TensorSliceLayer(margin=1)
pred_up1 = DeconvolutionalLayer(self.num_classes,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='pred_up1')
pred_up2_1 = DeconvolutionalLayer(self.num_classes * 2,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='pred_up2_1')
pred_up2_2 = DeconvolutionalLayer(self.num_classes * 2,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='pred_up2_2')
pred_up3_1 = DeconvolutionalLayer(self.num_classes * 4,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='pred_up3_1')
pred_up3_2 = DeconvolutionalLayer(self.num_classes * 4,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
with_bn=self.acti_func != 'selu',
name='pred_up3_2')
final_pred = ConvLayer(self.num_classes,
kernel_size=[1, 3, 3],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
name='final_pred')
f1 = images
f1 = block1_1(f1, is_training=is_training)
f1 = block1_2(f1, is_training=is_training)
f1 = fuse1(f1, is_training=is_training)
f1 = downsample1(f1, is_training=is_training)
if self.base_chns[0] != self.base_chns[1]:
f1 = feature_expand1(f1, is_training=is_training)
f1 = block2_1(f1, is_training=is_training)
f1 = block2_2(f1, is_training=is_training)
f1 = fuse2(f1, is_training=is_training)
f2 = downsample2(f1, is_training=is_training)
if self.base_chns[1] != self.base_chns[2]:
f2 = feature_expand2(f2, is_training=is_training)
f2 = block3_1(f2, is_training=is_training)
f2 = block3_2(f2, is_training=is_training)
f2 = block3_3(f2, is_training=is_training)
f2 = fuse3(f2, is_training=is_training)
f3 = f2
if self.base_chns[2] != self.base_chns[3]:
f3 = feature_expand3(f3, is_training)
f3 = block4_1(f3, is_training=is_training)
f3 = block4_2(f3, is_training=is_training)
f3 = block4_3(f3, is_training=is_training)
f3 = fuse4(f3, is_training=is_training)
p1 = centra_slice1(f1)
p1 = pred_up1(p1, is_training=is_training)
p2 = centra_slice2(f2)
p2 = pred_up2_1(p2, is_training=is_training)
p2 = pred_up2_2(p2, is_training=is_training)
p3 = pred_up3_1(f3, is_training=is_training)
p3 = pred_up3_2(p3, is_training=is_training)
cat = tf.concat([p1, p2, p3], axis=4, name='concate')
pred = final_pred(cat)
return pred
def layer_op(self, codes, is_training):
# Define the decoding fully-connected layers
decoders_fc = []
for i in range(0, len(self.layer_sizes_decoder)):
decoders_fc.append(FullyConnectedLayer(
n_output_chns=self.layer_sizes_decoder[i],
with_bias=True,
with_bn=True,
acti_func=self.acti_func_decoder[i],
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='decoder_fc_{}'.format(self.layer_sizes_decoder[i])))
print(decoders_fc[-1])
# Define the decoding convolutional layers
decoders_cnn = []
decoders_upsamplers = []
for i in range(0, len(self.trans_conv_output_channels)):
if self.upsampling_mode == 'DECONV':
decoders_upsamplers.append(DeconvolutionalLayer(
n_output_chns=self.trans_conv_output_channels[i],
kernel_size=self.trans_conv_unpooling_factors[i],
stride=self.trans_conv_unpooling_factors[i],
padding='SAME',
with_bias=True,
with_bn=True,
w_initializer=self.initializers['w'],
w_regularizer=None,
acti_func=None,
name='decoder_upsampler_{}_{}'.format(
self.trans_conv_unpooling_factors[i],
self.trans_conv_unpooling_factors[i])))
print(decoders_upsamplers[-1])
decoders_cnn.append(DeconvolutionalLayer(
n_output_chns=self.trans_conv_output_channels[i],
kernel_size=self.trans_conv_kernel_sizes[i],
stride=1,
padding='SAME',
with_bias=True,
with_bn=True,
#with_bn=not (i == len(self.trans_conv_output_channels) - 1),
# No BN on output
w_initializer=self.initializers['w'],
w_regularizer=None,
acti_func=self.acti_func_trans_conv[i],
name='decoder_trans_conv_{}_{}'.format(
self.trans_conv_kernel_sizes[i],
self.trans_conv_output_channels[i])))
print(decoders_cnn[-1])
# Fully-connected decoder layers
flow = codes
for i in range(0, len(self.layer_sizes_decoder)):
flow = decoders_fc[i](flow, is_training)
# Reconstitute the feature maps
flow = tf.reshape(flow, [-1] + self.downsampled_shape)
# Convolutional decoder layers
for i in range(0, len(self.trans_conv_output_channels)):
if self.upsampling_mode == 'DECONV':
flow = decoders_upsamplers[i](flow, is_training)
elif self.upsampling_mode == 'CHANNELWISE_DECONV':
flow = UpSampleLayer(
'CHANNELWISE_DECONV',
kernel_size=self.trans_conv_unpooling_factors[i],
stride=self.trans_conv_unpooling_factors[i])(flow)
elif self.upsampling_mode == 'REPLICATE':
flow = UpSampleLayer(
'REPLICATE',
kernel_size=self.trans_conv_unpooling_factors[i],
stride=self.trans_conv_unpooling_factors[i])(flow)
flow = decoders_cnn[i](flow, is_training)
return flow
def layer_op(self, images, is_training, layer_id=-1):
assert (layer_util.check_spatial_dims(
images, lambda x: x % 8 == 0))
# go through self.layers, create an instance of each layer
# and plugin data
layer_instances = []
### first convolution layer
params = self.layers[0]
first_conv_layer = ConvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
stride=2,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = first_conv_layer(images, is_training)
layer_instances.append((first_conv_layer, flow))
### resblocks, all kernels dilated by 1 (normal convolution)
params = self.layers[1]
with DilatedTensor(flow, dilation_factor=1) as dilated:
for j in range(params['repeat']):
res_block = HighResBlock(
params['n_features'],
params['kernels'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='%s_%d' % (params['name'], j))
dilated.tensor = res_block(dilated.tensor, is_training)
layer_instances.append((res_block, dilated.tensor))
flow = dilated.tensor
### resblocks, all kernels dilated by 2
params = self.layers[2]
with DilatedTensor(flow, dilation_factor=2) as dilated:
for j in range(params['repeat']):
res_block = HighResBlock(
params['n_features'],
params['kernels'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='%s_%d' % (params['name'], j))
dilated.tensor = res_block(dilated.tensor, is_training)
layer_instances.append((res_block, dilated.tensor))
flow = dilated.tensor
### resblocks, all kernels dilated by 4
params = self.layers[3]
with DilatedTensor(flow, dilation_factor=4) as dilated:
for j in range(params['repeat']):
res_block = HighResBlock(
params['n_features'],
params['kernels'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='%s_%d' % (params['name'], j))
dilated.tensor = res_block(dilated.tensor, is_training)
layer_instances.append((res_block, dilated.tensor))
flow = dilated.tensor
### 1x1x1 convolution layer
params = self.layers[4]
fc_layer = ConvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = fc_layer(flow, is_training)
layer_instances.append((fc_layer, flow))
### 3x3x3 deconvolution layer
params = self.layers[4]
fc_layer = DeconvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=3,
stride=2,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='deconv')
flow = fc_layer(flow, is_training)
layer_instances.append((fc_layer, flow))
### 1x1x1 convolution layer
params = self.layers[5]
fc_layer = ConvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
acti_func=None,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = fc_layer(flow, is_training)
layer_instances.append((fc_layer, flow))
# set training properties
if is_training:
self._print(layer_instances)
return layer_instances[-1][1]
return layer_instances[layer_id][1]
def layer_op(self, images, is_training, bn_momentum=0.9, layer_id=-1):
# image_size should be divisible by 8
# spatial_dims = images.get_shape()[1:-1].as_list()
# assert (spatial_dims[-2] % 16 == 0 )
# assert (spatial_dims[-1] % 16 == 0 )
block1 = UNetBlock((self.n_features[0], self.n_features[0]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B1')
block2 = UNetBlock((self.n_features[1], self.n_features[1]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B2')
block3 = UNetBlock((self.n_features[2], self.n_features[2]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B3')
block4 = UNetBlock((self.n_features[3], self.n_features[3]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B4')
block5 = UNetBlock((self.n_features[4], self.n_features[4]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B5')
block6 = UNetBlock((self.n_features[3], self.n_features[3]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B6')
block7 = UNetBlock((self.n_features[2], self.n_features[2]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B7')
block8 = UNetBlock((self.n_features[1], self.n_features[1]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B8')
block9 = UNetBlock((self.n_features[0], self.n_features[0]),
((1, 3, 3), (1, 3, 3)),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B9')
conv = ConvLayer(n_output_chns=self.num_classes,
kernel_size=(1, 1, 1),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
with_bias=True,
name='conv')
down1 = DownSampleLayer('MAX',
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='down1')
down2 = DownSampleLayer('MAX',
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='down2')
down3 = DownSampleLayer('MAX',
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='down3')
down4 = DownSampleLayer('MAX',
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='down4')
up1 = DeconvolutionalLayer(n_output_chns=self.n_features[3],
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='up1')
up2 = DeconvolutionalLayer(n_output_chns=self.n_features[2],
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='up2')
up3 = DeconvolutionalLayer(n_output_chns=self.n_features[1],
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='up3')
up4 = DeconvolutionalLayer(n_output_chns=self.n_features[0],
kernel_size=(1, 2, 2),
stride=(1, 2, 2),
name='up4')
f1 = block1(images, is_training, bn_momentum)
d1 = down1(f1)
f2 = block2(d1, is_training, bn_momentum)
d2 = down2(f2)
f3 = block3(d2, is_training, bn_momentum)
d3 = down3(f3)
f4 = block4(d3, is_training, bn_momentum)
d4 = down4(f4)
f5 = block5(d4, is_training, bn_momentum)
# add dropout to the original version
f5 = tf.nn.dropout(f5, self.dropout)
f5up = up1(f5, is_training, bn_momentum)
f4cat = tf.concat((f4, f5up), axis=-1)
f6 = block6(f4cat, is_training, bn_momentum)
# add dropout to the original version
f6 = tf.nn.dropout(f6, self.dropout)
f6up = up2(f6, is_training, bn_momentum)
f3cat = tf.concat((f3, f6up), axis=-1)
f7 = block7(f3cat, is_training, bn_momentum)
# add dropout to the original version
f7 = tf.nn.dropout(f7, self.dropout)
f7up = up3(f7, is_training, bn_momentum)
f2cat = tf.concat((f2, f7up), axis=-1)
f8 = block8(f2cat, is_training, bn_momentum)
# add dropout to the original version
f8 = tf.nn.dropout(f8, self.dropout)
f8up = up4(f8, is_training, bn_momentum)
f1cat = tf.concat((f1, f8up), axis=-1)
f9 = block9(f1cat, is_training, bn_momentum)
# add dropout to the original version
f9 = tf.nn.dropout(f9, self.dropout)
output = conv(f9)
return output
def layer_op(self, images, is_training=True, layer_id=-1, **unused_kwargs):
assert (layer_util.check_spatial_dims(images, lambda x: x % 8 == 0))
layer_instances = []
images2 = CubicResizeLayer((16, 16, 16))(images)
params = self.layers[0]
first_conv_layer = ConvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
with_bias=True,
with_bn=False,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = first_conv_layer(images2, is_training)
layer_instances.append((first_conv_layer, flow))
params = self.layers[1]
conv_layer = ConvolutionalLayer(n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
with_bias=True,
with_bn=False,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = conv_layer(flow, is_training)
layer_instances.append((conv_layer, flow))
params = self.layers[2]
for j in range(params['repeat']):
conv_layer = ConvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
with_bias=True,
with_bn=False,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='%s_%d' % (params['name'], j))
flow = conv_layer(flow, is_training)
layer_instances.append((conv_layer, flow))
params = self.layers[3]
conv_layer = ConvolutionalLayer(n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
with_bias=True,
with_bn=False,
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = conv_layer(flow, is_training)
layer_instances.append((conv_layer, flow))
params = self.layers[4]
deconv_layer = DeconvolutionalLayer(
n_output_chns=params['n_features'],
kernel_size=params['kernel_size'],
stride=2,
padding='SAME',
with_bias=True,
with_bn=False,
acti_func=None,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name=params['name'])
flow = deconv_layer(flow, is_training)
layer_instances.append((deconv_layer, flow))
if is_training:
self._print(layer_instances)
return layer_instances[-1][1]
return layer_instances[layer_id][1]
def layer_op(self, images, is_training):
block1_1 = ResBlock(self.base_chns[0],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block1_1')
block1_2 = ResBlock(self.base_chns[0],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block1_2')
block2_1 = ResBlock(self.base_chns[1],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block2_1')
block2_2 = ResBlock(self.base_chns[1],
kernels=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block2_2')
block3_1 = ResBlock(self.base_chns[2],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 1, 1], [1, 1, 1]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block3_1')
block3_2 = ResBlock(self.base_chns[2],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 2, 2], [1, 2, 2]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block3_2')
block4_1 = ResBlock(self.base_chns[3],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 3, 3], [1, 3, 3]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block4_1')
block4_2 = ResBlock(self.base_chns[3],
kernels=[[1, 3, 3], [1, 3, 3]],
dilation_rates=[[1, 2, 2], [1, 2, 2]],
acti_func=self.acti_func,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
name='block4_2')
fuse1 = ConvolutionalLayer(
self.base_chns[0],
kernel_size=[3, 1, 1], # Convolution on intra layers
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='fuse1')
downsample1 = ConvolutionalLayer(self.base_chns[0],
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='downsample1')
fuse2 = ConvolutionalLayer(self.base_chns[1],
kernel_size=[3, 1, 1],
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='fuse2')
downsample2 = ConvolutionalLayer(self.base_chns[1],
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='downsample2')
fuse3 = ConvolutionalLayer(self.base_chns[2],
kernel_size=[3, 1, 1],
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='fuse3')
fuse4 = ConvolutionalLayer(self.base_chns[3],
kernel_size=[3, 1, 1],
padding='VALID',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='fuse4')
feature_expand1 = ConvolutionalLayer(
self.base_chns[1], # Output channels
kernel_size=[1, 1, 1],
stride=[1, 1, 1],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='feature_expand1')
feature_expand2 = ConvolutionalLayer(
self.base_chns[2],
kernel_size=[1, 1, 1],
stride=[1, 1, 1],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='feature_expand2')
feature_expand3 = ConvolutionalLayer(
self.base_chns[3],
kernel_size=[1, 1, 1],
stride=[1, 1, 1],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='feature_expand3')
centra_slice1 = TensorSliceLayer(margin=2)
centra_slice2 = TensorSliceLayer(margin=1)
image_resize1 = ImageResize()
image_resize2 = ImageResize()
pred_up1 = DeconvolutionalLayer(self.num_classes,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='pred_up1')
pred_up2_1 = DeconvolutionalLayer(self.num_classes * 2,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='pred_up2_1')
pred_up2_2 = DeconvolutionalLayer(self.num_classes * 2,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='pred_up2_2')
pred_up3_1 = DeconvolutionalLayer(self.num_classes * 4,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='pred_up3_1')
pred_up3_2 = DeconvolutionalLayer(self.num_classes * 4,
kernel_size=[1, 3, 3],
stride=[1, 2, 2],
padding='SAME',
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
acti_func=self.acti_func,
name='pred_up3_2')
final_pred = ConvLayer(
self.num_classes, # Output two class: target and background
kernel_size=[1, 3, 3],
padding=
'SAME', # Same: keep shape; Valid: only get pixels with valid calculation.
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
b_initializer=self.initializers['b'],
b_regularizer=self.regularizers['b'],
name='final_pred')
f1 = images
f1 = block1_1(f1, is_training)
f1 = block1_2(f1, is_training)
f1 = fuse1(f1, is_training)
f1 = downsample1(f1, is_training)
img_resize1 = image_resize1(images, f1)
img_resize1 = centra_slice2(img_resize1)
f1 = tf.concat([img_resize1, f1], axis=4, name='concate')
if (self.base_chns[0] != self.base_chns[1]):
f1 = feature_expand1(
f1, is_training
) # To keep same channel number in cascaded netblocks
f1 = block2_1(f1, is_training)
f1 = block2_2(f1, is_training)
f1 = fuse2(f1, is_training)
f2 = downsample2(f1, is_training)
img_resize2 = image_resize2(images, f2)
img_resize2 = centra_slice1(img_resize2)
f2 = tf.concat([img_resize2, f2], axis=4, name='concate')
if (self.base_chns[1] != self.base_chns[2]):
f2 = feature_expand2(f2, is_training)
f2 = block3_1(f2, is_training)
f2 = block3_2(f2, is_training)
f2 = fuse3(f2, is_training)
f3 = f2
if (self.base_chns[2] != self.base_chns[3]):
f3 = feature_expand3(f3, is_training)
f3 = block4_1(f3, is_training)
f3 = block4_2(f3, is_training)
f3 = fuse4(f3, is_training)
p1 = centra_slice1(f1)
p1 = pred_up1(p1, is_training)
p2 = centra_slice2(f2)
p2 = pred_up2_1(p2, is_training)
p2 = pred_up2_2(p2, is_training)
p3 = pred_up3_1(f3, is_training)
p3 = pred_up3_2(p3, is_training)
cat = tf.concat([p1, p2, p3], axis=4, name='concate')
pred = final_pred(cat)
return pred
def layer_op(self, images, is_training, bn_momentum=0.9, layer_id=-1):
block1 = FCNBlock((self.n_features[0], self.n_features[0]),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B1')
block2 = FCNBlock((self.n_features[1], self.n_features[1]),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B2')
block3 = FCNBlock(
(self.n_features[2], self.n_features[2], self.n_features[2]),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B3')
block4 = FCNBlock(
(self.n_features[3], self.n_features[3], self.n_features[3]),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B4')
block5 = FCNBlock(
(self.n_features[4], self.n_features[4], self.n_features[4]),
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='B5')
conv6 = ConvolutionalLayer(n_output_chns=self.n_features[-1] * 2,
kernel_size=[1, 3, 3],
with_bias=True,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='conv6')
conv7 = ConvolutionalLayer(n_output_chns=self.n_features[-1] * 2,
kernel_size=[1, 1, 1],
with_bias=True,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=self.acti_func,
name='conv7')
conv_score3 = ConvolutionalLayer(n_output_chns=self.num_classes,
kernel_size=[1, 3, 3],
with_bias=True,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=None,
name='score3')
conv_score4 = ConvolutionalLayer(n_output_chns=self.num_classes,
kernel_size=[1, 3, 3],
with_bias=True,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=None,
name='score4')
conv_score5 = ConvolutionalLayer(n_output_chns=self.num_classes,
kernel_size=[1, 3, 3],
with_bias=True,
w_initializer=self.initializers['w'],
w_regularizer=self.regularizers['w'],
acti_func=None,
name='score5')
up1 = DeconvolutionalLayer(n_output_chns=self.num_classes,
kernel_size=(1, 4, 4),
stride=(1, 2, 2),
with_bias=True,
acti_func=None,
name='up1')
up2 = DeconvolutionalLayer(n_output_chns=self.num_classes,
kernel_size=(1, 4, 4),
stride=(1, 2, 2),
with_bias=True,
acti_func=None,
name='up2')
up3 = DeconvolutionalLayer(n_output_chns=self.num_classes,
kernel_size=(1, 16, 16),
stride=(1, 8, 8),
with_bias=True,
acti_func=None,
name='up3')
f1 = block1(images, is_training, bn_momentum)
f2 = block2(f1, is_training, bn_momentum)
f3 = block3(f2, is_training, bn_momentum)
f3 = tf.nn.dropout(f3, self.dropout)
f4 = block4(f3, is_training, bn_momentum)
f4 = tf.nn.dropout(f4, self.dropout)
f5 = block5(f4, is_training, bn_momentum)
f5 = tf.nn.dropout(f5, self.dropout)
f6 = conv6(f5, is_training, bn_momentum)
f6 = tf.nn.dropout(f6, self.dropout)
f7 = conv7(f6, is_training, bn_momentum)
f7 = tf.nn.dropout(f7, self.dropout)
score3 = conv_score3(f3, is_training, bn_momentum)
score4 = conv_score4(f4, is_training, bn_momentum)
score5 = conv_score5(f7, is_training, bn_momentum)
pred = up1(score5, is_training, bn_momentum)
pred = pred + score4
pred = up2(pred, is_training, bn_momentum)
pred = pred + score3
pred = up3(pred, is_training, bn_momentum)
return pred
